The biggest point to set gaps I found was the door shut pillar, the panel next to your shoulder if you were sitting in the car, that normally is a fixed point and basically everything is dictated by it. In my case I replaced a rusty lower section of it and ended up with the newer section slightly to the rear which made getting decent gaps impossible. Had to cut the weld and move it forward, which ended up doing the trick. Dry fit the rear / front and doors, check your gaps and adjust from there, surprisingly the rear will come forward somewhat but the pillar has to be re-anchored strongly when you get the best location.